On Uncommon Descent, poster gpuccio has been discussing “functional information”. Most of gpuccio’s argument is a conventional “islands of function” argument. Not being very knowledgeable about biochemistry, I’ll happily leave that argument to others.
But I have been intrigued by gpuccio’s use of Functional Information, in particular gpuccio’s assertion that if we observe 500 bits of it, that this is a reliable indicator of Design, as here, about at the 11th sentence of point (a):
… the idea is that if we observe any object that exhibits complex functional information (for example, more than 500 bits of functional information ) for an explicitly defined function (whatever it is) we can safely infer design.
I wonder how this general method works. As far as I can see, it doesn’t work. There would be seem to be three possible ways of arguing for it, and in the end; two don’t work and one is just plain silly. Which of these is the basis for gpuccio’s statement? Let’s investigate …
A quick summary
Let me list the three ways, briefly.
(1) The first is the argument using William Dembski’s (2002) Law of Conservation of Complex Specified Information. I have argued (2007) that this is formulated in such a way as to compare apples to oranges, and thus is not able to reject normal evolutionary processes as explanations for the “complex” functional information. In any case, I see little sign that gpuccio is using the LCCSI.
(2) The second is the argument that the functional information indicates that only an extremely small fraction of genotypes have the desired function, and the rest are all alike in totally lacking any of this function. This would prevent natural selection from following any path of increasing fitness to the function, and the rareness of the genotypes that have nonzero function would prevent mutational processes from finding them. This is, as far as I can tell, gpuccio’s islands-of-function argument. If such cases can be found, then explaining them by natural evolutionary processes would indeed be difficult. That is gpuccio’s main argument, and I leave it to others to argue with its application in the cases where gpuccio uses it. I am concerned here, not with the islands-of-function argument itself, but with whether the design inference from 500 bits of functional information is generally valid.
We are asking here whether, in general, observation of more than 500 bits of functional information is “a reliable indicator of design”. And gpuccio’s definition of functional information is not confined to cases of islands of function, but also includes cases where there would be a path to along which function increases. In such cases, seeing 500 bits of functional information, we cannot conclude from this that it is extremely unlikely to have arisen by normal evolutionary processes. So the general rule that gpuccio gives fails, as it is not reliable.
(3) The third possibility is an additional condition that is added to the design inference. It simply declares that unless the set of genotypes is effectively unreachable by normal evolutionary processes, we don’t call the pattern “complex functional information”. It does not simply define “complex functional information” as a case where we can define a level of function that makes probability of the set less than 
. That additional condition allows us to safely conclude that normal evolutionary forces can be dismissed — by definition. But it leaves the reader to do the heavy lifting, as the reader has to determine that the set of genotypes has an extremely low probability of being reached. And once they have done that, they will find that the additional step of concluding that the genotypes have “complex functional information” adds nothing to our knowledge. CFI becomes a useless add-on that sounds deep and mysterious but actually tells you nothing except what you already know. So CFI becomes useless. And there seems to be some indication that gpuccio does use this additional condition.
Let us go over these three possibilities in some detail. First, what is the connection of gpuccio’s “functional information” to Jack Szostak’s quantity of the same name?
Is gpuccio’s Functional Information the same as Szostak’s Functional Information?
gpuccio acknowledges that gpuccio’s definition of Functional Information is closely connected to Jack Szostak’s definition of it. gpuccio notes here:
Please, not[e] the definition of functional information as:
“the fraction of all possible configurations of the system that possess a degree of function >=
Ex.”which is identical to my definition, in particular my definition of functional information as the
upper tail of the observed function, that was so much criticized by DNA_Jock.
(I have corrected gpuccio’s typo of “not” to “note”, JF)
We shall see later that there may be some ways in which gpuccio’s definition
is modified from Szostak’s. Jack Szostak and his co-authors never attempted any use of his definition to infer Design. Nor did Leslie Orgel, whose Specified Information (in his 1973 book The Origins of Life) preceded Szostak’s. So the part about design inference must come from somewhere else.
gpuccio seems to be making one of three possible arguments;
Possibility #1 That there is some mathematical theorem that proves that ordinary evolutionary processes cannot result in an adaptation that has 500 bits of Functional Information.
Use of such a theorem was attempted by William Dembski, his Law of Conservation of Complex Specified Information, explained in Dembski’s book No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence (2001). But Dembski’s LCCSI theorem did not do what Dembski needed it to do. I have explained why in my own article on Dembski’s arguments (here). Dembski’s LCCSI changed the specification before and after evolutionary processes, and so he was comparing apples to oranges.
In any case, as far as I can see gpuccio has not attempted to derive gpuccio’s argument from Dembski’s, and gpuccio has not directly invoked the LCCSI, or provided a theorem to replace it. gpuccio said in a response to a comment of mine at TSZ,
Look, I will not enter the specifics of your criticism to Dembski. I agre with Dembski in most things, but not in all, and my arguments are however more focused on empirical science and in particular biology.
While thus disclaiming that the argument is Dembski’s, on the other hand gpuccio does associate the argument with Dembski here by saying that
Of course, Dembski, Abel, Durston and many others are the absolute references for any discussion about functional information. I think and hope that my ideas are absolutely derived from theirs. My only purpose is to detail some aspects of the problem.
and by saying elsewhere that
No generation of more than 500 bits has ever been observed to arise in a non design system (as you know, this is the fundamental idea in ID).
That figure being Dembski’s, this leaves it unclear whether gpuccio is or is not basing the argument on Dembski’s. But gpuccio does not directly invoke the LCCSI, or try to come up with some mathematical theorem that replaces it.
So possibility #1 can be safely ruled out.
Possibility #2. That the target region in the computation of Functional Information consists of all of the sequences that have nonzero function, while all other sequences have zero function. As there is no function elsewhere, natural selection for this function then cannot favor sequences closer and closer to the target region.
Such cases are possible, and usually gpuccio is talking about cases like this. But gpuccio does not require them in order to have Functional Information. gpuccio does not rule out that the region could be defined by a high level of function, with lower levels of function in sequences outside of the region, so that there could be paths allowing evolution to reach the target region of sequences.
An example in which gpuccio recognizes that lower levels of function can exist outside the target region is found here, where gpuccio is discussing natural and artificial selection:
Then you can ask: why have I spent a lot of time discussing how NS (and AS) can in some cases add some functional information to a sequence (see my posts #284, #285 and #287)
There is a very good reason for that, IMO.
I am arguing that:
1) It is possible for NS to add some functional information to a sequence, in a few very specific cases, but:
2) Those cases are extremely rare exceptions, with very specific features, and:
3) If we understand well what are the feature that allow, in those exceptional cases, those limited “successes” of NS, we can easily demonstrate that:
4) Because of those same features that allow the intervention of NS, those scenarios can never, never be steps to complex functional information.
Jack Szostak defined functional information by having us define a cutoff level of function to define a set of sequences that had function greater than that, without any condition that the other sequences had zero function. Neither did Durston. And as we’ve seen gpuccio associates his argument with theirs.
So this second possibility could not be the source of gpuccio’s general assertion about 500 bits of functional information being a reliable indicator of design, however much gpuccio concentrates on such cases.
Possibility #3. That there is an additional condition in gpuccio’s Functional Information, one that does not allow us to declare it to be present if there is a way for evolutionary processes to achieve that high a level of function. In short, if we see 500 bits of Szostak’s functional information, and if it can be put into the genome by natural evolutionary processes such as natural selection then for that reason we declare that it is not really Functional Information. If gpuccio is doing this, then gpuccio’s Functional Information is really a very different animal than Szostak’s functional information.
Is gpuccio doing that? gpuccio does associate his argument with William Dembski’s, at least in some of his statements. And William Dembski has defined his Complex Specified Information in this way, adding the condition that it is not really CSI unless it is sufficiently improbable that it be achieved by natural evolutionary forces (see my discussion of this here in the section on “Dembski’s revised CSI argument” that refer to Dembski’s statements here). And Dembski’s added condition renders use of his CSI a useless afterthought to the design inference.
gpuccio does seem to be making a similar condition. Dembski’s added condition comes in via the calculation of the “probability” of each genotype. In Szostak’s definition, the probabilities of sequences are simply their frequencies among all possible sequences, with each being counted equally. In Dembski’s CSI calculation, we are instead supposed to compute the probability of the sequence given all evolutionary processes, including natural selection.
gpuccio has a similar condition in the requirements for concluding that complex
functional information is present: We can see it at step (6) here:
If our conclusion is yes, we must still do one thing. We observe carefully the object and what we know of the system, and we ask if there is any known and credible algorithmic explanation of the sequence in that system. Usually, that is easily done by excluding regularity, which is easily done for functional specification. However, as in the particular case of functional proteins a special algorithm has been proposed, neo darwininism, which is intended to explain non regular functional sequences by a mix of chance and regularity, for this special case we must show that such an explanation is not credible, and that it is not supported by facts. That is a part which I have not yet discussed in detail here. The necessity part of the algorithm (NS) is not analyzed by dFSCI alone, but by other approaches and considerations. dFSCI is essential to evaluate the random part of the algorithm (RV). However, the short conclusion is that neo darwinism is not a known and credible algorithm which can explain the origin of even one protein superfamily. It is neither known nor credible. And I am not aware of any other algorithm ever proposed to explain (without design) the origin of functional, non regular sequences.
In other words, you, the user of the concept, are on your own. You have to rule out that natural selection (and other evolutionary processes) could reach the target sequences. And once you have ruled it out, you have no real need for the declaration that complex functional information is present.
I have gone on long enough. I conclude that the rule that observation of 500 bits of functional information is present allows us to conclude in favor of Design (or at any rate, to rule out normal evolutionary processes as the source of the adaptation) is simply nonexistent. Or if it does exist, it is as a useless add-on to an argument that draws that conclusion for some other reason, leaving the really hard work to the user.
Let’s end by asking gpuccio some questions:
1. Is your “functional information” the same as Szostak’s?
2. Or does it add the requirement that there be no function in sequences that
are outside of the target set?
3. Does it also require us to compute the probability that the sequence arises as a result of normal evolutionary processes?
Corneel,
We can add invertebrates to the analysis.
In the case where selection does occur it is preserving the sequence.
Belgium saison is one of my favorites.
This dancing may be a rare event as when an animal is never born there is no time to dance 🙁
Corneel,
However making an estimate as Axe and Hayashi did creates no safety concerns 🙂
Right, that would get us an exhaustive list of all multicellular organisms. We wouldn’t be forgetting any, would we?
Corneel,
And plants also.. Whatever floats your boat 🙂
Those are some blinders you’ve got on, you know that?
Corneel,
We can keep going all day long with you arguing against yourself.
You are still going to have to explain why there is more variation outside the vertebrate sub phylum. Could it be…..wait for it…..different functional requirements.
Yes, there are different functional requirements. And those functional requirements were created by intelligent agents.
We humans (normally considered intelligent agents) created those functional requirements after the fact, as a part of our pseudo-explanations.
Or, to say it differently, those “functional requirements” are not requirements at all. They are merely attributions.
Why do you say that? I don’t think you can have read Rumraket’s OP
The fatal blow is that Axe did not do what he claimed to have done.
That was rhetorical, BTW. As KN might say, my days of not taking you seriously are coming to a middle.
Neil Rickert,
It really doesn’t matter how you try to put an evolutionist spin on what we are observing. At the end of the day it is a functional organism. The Neo-Darwinists have no explanation of how all these proteins are observed in optimized sequence states such that mutational variation over long periods of time is unexplainably low.
The only known cause of optimized sequences is conscious intelligence.
Alan Fox,
What did he claim to have done?
colewd,
Haven’t you read Axe either?
Alan Fox,
Sure. I have read both and I have read Hunt’s paper. Axe was very careful to explain his experimental methods. Art Hunt acknowledges this in his paper.
Rumraket tries to make a genetic argument like you do with the pebbles but this is not relevant when evaluating gpuccio’s work as FI measures a specific function. The most talked about is the beta chain of ATP synthase. Rumraket is making the “any function” argument.
Rumraket compared Axe’s work with other experiments on different proteins. This is comparing different functional information.
Hunt accepted Axes results as in the ball park of other experiments.
Why are you asking him? Alan doesn’t know.
I bet gpuccio disagrees. 🙂
Are those mushrooms safe to view?
And the genotype. And everything in between. Lo, the miraculous powers.
I think Bill has managed to convince himself that we are arguing with him because he’s making good points worthy of debate (“they’re responding to me, that must mean I’m on to something”), rather than the actual reason: We’re trying to teach him concepts he keeps proving he doesn’t understand.
No, it’s not God’s fault that you don’t know.
They forgot to use scare quotes.
ETA: Perhaps they should have used protein engineering instead of protein design, lest someone get the mistaken notion that design was involved.
Splitting lineages resulting in reproductive isolation of continually mutating lineages leads to divergence at a rate affected by mutation rate, population size, and the level of purifying selection, with the magnitude of divergence positively correlated with the time since divergence.
That’s it. That fully and completely explains what we see.
And here is that explanation:
Rumraket,
Nice assertion.
Omfg how can you not understand this Bill? What the hell is wrong with you? Why isn’t this super simple concept apparent to you?
In general, the deeper the node that connects two branches, the more divergent the sequences represented by the ends of those branches.
That’s why SOME bacteria will look very divergent from each other (they diverged longer ago), while OTHER bacteria will look much more similar (they diverged more recently). That’s why all of vertebrates are more similar to each other than they are to plants, or to fungi. That’s why all of fungi are more similar to each other. That’s why all plants are more similar to each other.
This general pattern is explained by the incremental and independent accumulation of change in isolated lineages at varying divergence times. It is immediately and completely explained by COMMON DESCENT.
How much are mine worth?
That would certainly explain why every DNA and RNA sequence has an affinity for ATP!
It’s not just an assertion given that I actually gave the explanation. I don’t merely name the explanation (like “evolution”) and then blindly declare the thing explained (like “evolution explains it).
If you actually understand the words I use (“lineage”, “splitting”, “isolation”, “accumulation”, “divergence”, etc.) you will see my post ipso facto constitutes an explanation and not just an assertion. But you have to actually think about what the words mean instead of blowing a fuse.
One cannot even fathom how of all the fallacies you could have decided to accuse me of you went for this one as I haven’t at any point claimed to be an authority, nor have I asserted that those who are authorities on the subject matter are automatically right by virtue of their titles. Ironically, I keep asking you to think for yourself.
Like, you couldn’t possibly have stuffed more wrong into your post. This is a world record. Your post contains entirely and only demonstrable falsehoods.
Get help!
Would you settle for YouTube videos?
Rumraket,
I am happy for you that you believe in Neo-Darwinism. It all looks really obvious to you. It doesn’t look obvious to me and other people. I think some of your explanations are beyond naive like the spliceosome was created by massive gene duplications. Or so was the ubiquitin system. How about the circulatory system or the central nervous system or the muscle skeletal system. All by separated populations and reproduction. Give me a fucking break.
I could go on but there is no point as you are committed to the evolutionary story.
Good thing we’re here to help you out with that. And I’m not even a biologist.
Rumraket,
.
Then why are you so fucking sure of yourself that this theory is the real explanation of life’s diversity
From you I always get a runaround.
I claimed what was not an evolutionary process?
And I was “naughty” for doing what?
Protein design is a design process. And protein engineering is an engineering process. And if evolutionary processes are design processes and/or engineering processes, then you guys have lost the debate.
Evolutionary processes do not select for a pre-desired, pre-specified outcome. IF they do, then they are teleological.
If you and Rumraket are ok with teleology in evolution you wan’t get a comp,aint from me about that. Just don’t pretend later that you reject teleology in evolution.
Rumraket:
colewd:
Because — unlike you — he is actually capable of thinking it through.
It’s that simple. Intelligence and knowledge are extremely valuable, Bill. Why do you suppose your God deprives you of both?
Like patience, persistence, frustration and how to be a dick?
She has a sense of humor and likes to feel superior.
Mung,
And she likes atheists much more than she likes Christians.
One who is probably correct in what they say on a particular topic is an authority on that particular topic
A is an authority on a particular topic
A says something about that topic
A is probably correct
Given that atheists are like little children.
Excellent choice, BTW (I thought you guys called it “farmhouse”)
am not!
No, only the phenotype. If there is no phenotypic variation, then there cannot be fitness variation either, and therefore no selection.
The answer has not changed since the last time you asked me this question.
So we can add your “runaround” claim to the list of Mung’s falsehoods.
Are TE’s, like you, little children who still believe in Santa then?
Am too! Children are at least open minded by default. Hence the desire by the nonsense purveyors to get em early.
Evolution can’t be teleological. I don’t mean by definition, it’s simply obvious looking at the evidence.
Let’s say you were god, and you knew at some point in the past, let’s say 300M years ago, that you wanted to produce some extant species. How long would it take you to produce your desired result? Even if you work with completely random mutations and you only do the selection, it would take you a lot less time than what it actually took.
There’s no spooky ghost in the sky messing with evolutionary processes, Mung. Deal with it
I’ll remember that the next time you employ hyperbole. ok, so I don’t always get the runaround from you. But enough to make it very annoying.
And you didn’t answer my question:
And I was “naughty” for doing what?
And you didn’t address my other comments.
So yeah, runaround.
I wasn’t being naughty, so we’ll add that to your list of your falsehoods.
No Mung,
I did answer your question. You claimed that the process Rumraket described was not an evolutionary process, and then, when he corrected you, you pretended that you had not made such a claim, instead writing
I called you out on it. Since then, you have repeatedly asked what it was you did that was naughty, and I have repeatedly pointed you to the specific comments you made, where you appear to dissemble. I’m sure it is just an honest failure to understand on your part.
I did enjoy your bout of drive-by one-liners, though.
Because I understand at least some of the evidence for it, and understand how powerful that evidence is.
I’m pretty sure that I don’t need to be a recognized authority to be able to reason about a subject and have a willingess to learn about it.
Rumraket,
Fair enough. A very classy response. Even through we disagree on the strength of the evidence for the theory I do respect you candor, tenacity, and willingness to back up your claims. Thanks.
Corneel,
We do with the local brews but when origin is from Belgium we call is a saison.